Check for Back-Calculated Watershed Areas

The purpose of this document is to test the back-calculated watershed areas. All code will be drawn from the IWAM function vignette.

S1. Data Map

The following function vignette/example is from the IWAM Package Repo hosted publicly through the Pacific Salmon Assess organization available at this link.

The package currently utilizes the following data sets:

S2. Initialize function

IWAM_backcalc <- IWAM_func(WAin = "DataIn/Ordered_backcalculated_noagg.csv", # Data (INPUT)
                       # Ordered_backcalculated_noagg - ordered corrected to original input file
                       # Backcalc_targetstocks_NoAgg.csv - broken due to alphabetical ordering
                       remove.EnhStocks = FALSE, # Remove Enhancement stocks (INPUT)
                       run.bootstrap = TRUE, # TRUE/FALSE for running the bootstrap process
                       bs_seed = 1, # Change the internal seed for the bootstrap (INPUT)
                       bs_nBS = 20000, # Change the internal number of trials for the bootstrap (INPUT)
                       # Run 10 for testing purposes - otherwise 20000
                       plot = FALSE, # Print plots to DataOut/
                       est.table = FALSE # Store tables
)

S3. Check outputs

This code is a direct lift from the IWAM function vignette. Once the model and bootstrapping has completed, the function will store the following objects:

The following tables (1-3) have been prepared for comparison to Holt et al. (2023) Res Doc (Table 9). The table will also be stored in your repository folder under the name of “Backcalculation_stockestimates_table.csv”.

Table 1. SGEN, SREP, and SMSY estimates including 0.25% and 97.5% quantiles for all listed stocks. Watershed areas are back-calculated from Parken estimates with the exception of all WCVI stocks, which use original watershed areas: Nahmint, Sarita, Somass, Bedwell/Ursus, Cypre, Megin, Moyeha, Tranquil, Artlish, Kaouk, Tahsish, Nitinat, Burman, Conuma, Gold, Leiner, Tahsis, Zeballos, Cayeghle, Marble, San Juan, Canton Creek, Espinosa, Kauwinch River, Kleeptee, Little Zeballos River, Malksope River, McKay Cove Creek, Mooyah River, Ououkinsh River, Sucwoa River, Tlupana River, Tsowwin River.

SGEN, SREP, and SMSY Estimates for All Stocks
Stock WA SGEN SGEN LQ SGEN UQ SREP SREP LQ SREP UQ SMSY SMSY LQ SMSY UQ
South Thompson Agg 29565 94000 23000.00 320000 490000 230000 1000000 210000 99000.0 450000
Lower Shuswap 2663 8200 2100.00 25000 43000 24000 76000 18000 10000.0 33000
Middle Shuswap 640 2000 480.00 6000 10000 5700 18000 4400 2400.0 7800
Wap 20 57 13.00 210 300 130 710 130 53.0 310
East 46 130 32.00 470 710 330 1500 310 140.0 670
Goodspeed 15 41 9.20 160 220 88 540 94 37.0 240
Keith 56 160 38.00 560 860 400 1800 370 170.0 800
Klaskish 41 120 26.00 410 620 280 1400 270 120.0 590
Mahatta 114 340 80.00 1100 1800 890 3500 760 380.0 1500
Washlawlis 23 66 15.00 250 350 150 810 150 63.0 350
Colonial&Cayeagle 79 230 55.00 780 1200 590 2400 520 250.0 1100
Marble 168 500 120.00 1600 2600 1300 5000 1100 570.0 2200
Adam 279 830 210.00 2700 4400 2400 8000 1900 1000.0 3500
Amor de Cosmos 15 42 8.70 160 220 87 540 94 37.0 240
Cluxewe 90 260 62.00 870 1400 680 2800 600 290.0 1200
Kokish 104 310 74.00 1000 1600 810 3200 690 340.0 1400
Quatse 80 230 56.00 780 1200 600 2500 530 250.0 1100
Nimpkish (above Lake) 400 1200 300.00 3700 6300 3500 11000 2700 1500.0 5000
Salmon 912 2800 690.00 8400 15000 8200 26000 6300 3500.0 11000
Quinsam-Campbell 171 510 120.00 1600 2600 1400 5000 1100 580.0 2200
Conuma 20 57 12.00 210 300 130 720 130 53.0 310
Tahsis 77 230 54.00 760 1200 580 2500 510 250.0 1100
Burman 70 210 48.00 690 1100 520 2200 460 220.0 970
Artlish 64 190 44.00 630 970 460 2000 420 200.0 890
Kaouk 101 300 71.00 990 1600 780 3100 670 330.0 1400
Tahsish 172 520 120.00 1600 2700 1400 5100 1200 590.0 2200
Gold 856 2600 680.00 7800 14000 7800 24000 5900 3300.0 10000
Leiner 109 330 78.00 1100 1700 860 3300 730 360.0 1500
Zeballos 194 580 140.00 1800 3000 1600 5700 1300 680.0 2500
Amai 14 39 8.20 150 210 81 510 88 35.0 220
Canton 10 28 5.90 110 150 57 380 63 24.0 160
Espinosa 5 13 2.50 58 70 24 200 30 10.0 89
Hoiss 13 38 8.20 150 200 81 500 87 34.0 220
Kauwinch 44 130 29.00 450 670 310 1400 290 130.0 630
Kleeptee 14 40 8.80 150 210 85 520 90 36.0 230
Little Zeballos River 43 130 29.00 440 660 310 1500 280 130.0 640
Malksope 20 59 13.00 220 310 130 740 130 55.0 320
Mckay 1 4 0.68 20 21 6 75 9 2.6 32
Mooyah 8 22 4.40 88 120 43 310 50 18.0 140
Ououkinsh 17 47 10.00 180 250 100 620 110 43.0 270
Power 51 150 34.00 500 780 360 1700 340 150.0 730
Sucwoa 25 75 17.00 270 390 170 890 170 72.0 390
Tlupana 20 57 12.00 220 300 130 720 130 53.0 310
Tsowwin 26 75 16.00 270 400 170 910 170 73.0 400
Nitinat 357 1100 270.00 3300 5600 3000 10000 2400 1300.0 4500
San Juan 330 990 250.00 3000 5200 2800 9400 2200 1200.0 4100
Nahmint 42 120 28.00 420 640 290 1400 270 120.0 610
Sarita 84 250 59.00 830 1300 630 2700 560 270.0 1200
Bedwell 99 290 71.00 940 1500 780 3000 660 330.0 1300
Megin 245 730 180.00 2300 3800 2100 7100 1600 870.0 3100
Moyeha 116 340 83.00 1100 1800 900 3500 770 380.0 1500
Cypre 39 110 26.00 400 590 270 1300 250 110.0 570
Tranquil 12 35 7.40 130 180 74 460 79 31.0 200
Somass (stamp&sproat) 1057 3200 810.00 9800 17000 9600 30000 7200 4000.0 13000
Puntledge Falls 560 1700 430.00 5200 8800 5000 16000 3800 2100.0 6900
Englishman 299 890 220.00 2800 4700 2600 8500 2000 1100.0 3800
Big Qualicum 137 400 98.00 1300 2100 1100 4100 920 460.0 1800
Little Qualicum 95 280 66.00 910 1500 710 2900 630 300.0 1300
Puntledge Summers 433 1300 330.00 4000 6800 3800 12000 2900 1600.0 5400
Nanaimo Falls 545 1600 400.00 5100 8600 4800 15000 3700 2000.0 6800
Klinaklini 1475 4500 1100.00 14000 24000 13000 41000 10000 5600.0 18000
Maria Slough 31 89 20.00 310 460 210 1100 200 88.0 460
Homathko 286 860 210.00 2700 4500 2400 8300 1900 1000.0 3700
Okanagan 611 1900 470.00 5600 9600 5500 17000 4200 2300.0 7500
Ahnuhati 103 300 73.00 1000 1600 800 3200 690 340.0 1400
Apple 104 310 73.00 990 1600 800 3200 690 340.0 1400
Sim 24 70 16.00 250 370 160 850 160 67.0 380
Franklin 120 360 86.00 1200 1900 950 3700 800 400.0 1600
Southgate 179 530 130.00 1700 2800 1500 5300 1200 620.0 2300
Kakweiken 51 150 35.00 500 780 370 1700 340 160.0 730
Wakeman 305 910 230.00 2800 4800 2600 8900 2100 1100.0 3900
Kingcome 282 860 210.00 2600 4400 2400 8100 1900 1000.0 3600
Orford 38 110 25.00 380 570 260 1200 250 110.0 550
Stafford 21 60 13.00 220 320 130 740 140 57.0 330
Phillips 193 580 140.00 1800 3000 1600 5700 1300 670.0 2500
Brem 221 660 160.00 2100 3500 1900 6400 1500 780.0 2800
Indian 177 530 130.00 1700 2700 1500 5200 1200 610.0 2300
Quatam 147 440 110.00 1400 2300 1200 4400 980 490.0 1900
Seymour - Georgia Strait 55 160 38.00 560 850 400 1800 370 170.0 800
Theodosia 55 160 37.00 540 840 400 1800 360 170.0 770
Toba 450 1300 340.00 4200 7100 4000 13000 3100 1700.0 5600
Squamish 832 2500 640.00 7600 13000 7500 23000 5700 3200.0 10000
Goldstream 42 120 29.00 430 640 300 1400 280 120.0 620
Deadman 754 1000 250.00 3200 5400 2900 9900 2300 1200.0 4300
Nicola 6225 4100 1000.00 13000 22000 12000 40000 9300 4900.0 18000
Spius 614 890 210.00 2800 4600 2500 8600 2000 1100.0 3800
Coldwater 255 500 120.00 1600 2600 1400 4800 1100 590.0 2100
Louis 438 710 180.00 2200 3700 2000 6900 1600 840.0 3000
Bonaparte 3002 2600 630.00 8000 13000 7100 25000 5800 3000.0 11000
Bessette 232 470 120.00 1500 2400 1300 4600 1100 540.0 2000
Portage 454 730 180.00 2300 3800 2000 7000 1600 860.0 3100
Chilko 2103 2000 500.00 6300 11000 5800 19000 4500 2400.0 8400
Quesnel System (Cariboo) 3998 3100 760.00 9700 16000 8700 30000 6900 3700.0 13000
Nechako System (Stuart, Stellako) 15674 7600 1900.00 24000 40000 21000 75000 17000 8800.0 33000
Taseko 2219 2100 530.00 6500 11000 5900 20000 4700 2500.0 8800
Bridge 351 620 150.00 2000 3200 1700 6000 1400 720.0 2600
North Thompson and Tribs 5910 4000 970.00 13000 21000 11000 39000 9000 4700.0 17000
Upper Fraser Spring Agg 33079 13000 3100.00 41000 66000 34000 120000 28000 14000.0 55000
Birkenhead 462 740 190.00 2400 3900 2100 7200 1700 890.0 3200
Eagle 594 870 210.00 2700 4600 2400 8400 2000 1000.0 3700
Salmon @ Salmon Arm 638 920 220.00 2900 4800 2600 8900 2100 1100.0 3900
Seymour - South Thompson 79 230 56.00 720 1200 620 2300 510 260.0 1000
Endako 690 970 240.00 3000 5000 2700 9300 2200 1100.0 4100
Chilako 1908 1900 480.00 5900 9900 5400 18000 4300 2300.0 7900
Horsefly 487 770 190.00 2400 4000 2100 7300 1700 900.0 3200
Westroad, Baker, Naver, Narcosli, Cottonwood 8681 5200 1300.00 16000 27000 14000 50000 12000 6100.0 22000
Chilcotin (upper and lower) 1993 1900 480.00 6100 10000 5500 19000 4400 2300.0 8200
Driftwood 708 980 240.00 3000 5100 2800 9400 2200 1200.0 4100
Nadina 919 1200 290.00 3700 6100 3300 11000 2600 1400.0 4900
Upper Cariboo 554 830 200.00 2600 4300 2400 8000 1900 990.0 3500
Taseko (Spring Timing) Agg 2218 2100 530.00 6500 11000 5900 20000 4700 2500.0 8700
Nahatlatch 246 480 120.00 1500 2500 1400 4700 1100 570.0 2100
Upper Pitt 287 540 130.00 1700 2800 1500 5300 1200 630.0 2300
Big Silver 421 690 170.00 2200 3600 1900 6700 1600 820.0 3000
North Thompson Agg 2086 2000 500.00 6200 10000 5700 19000 4500 2400.0 8400

S4. Comparative Plotting

The objective of this section is to provide comparison figures between the IWAM function’s estimates of SMSY and SREP to the Parken model estimates. The following plots have been limited to a maximum Smsy and Srep value of 25,000 in order to match those of the technical working group presentations.